The matrix must be in this triangular form with the secondary structure order H E C T G S B 3 X 0 H E C T G S B 3 X 0 IMPORTANT: '0' is treated as wild character. This means that for '0' the open gap penalty is not increased (on the contrary to the other symbols). ### file example identity matrix (default) ### ### cut below this line ### 10 0 10 0 0 10 0 0 0 10 0 0 0 0 10 0 0 0 0 0 10 0 0 0 0 0 0 10 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 10 ### file example from Wallqvist et al. Bioinformatics 16:988 (2000) ### ### only H E C are considered ### ### cut below this line ### 2 -15 4 -4 -4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0